Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis
Danielle C. Lohman, Farhad Forouhar, Emily T. Beebe, Matthew S. Stefely, Catherine E. Minogue, Arne Ulbrich, Jonathan A. Stefely, Shravan Sukumar, Marta Luna-Sánchez, Adam Jochem, Scott Lew, Jayaraman Seetharaman, Rong Xiao, Huang Wang, Michael S. Westphall, Russell L. Wrobel, John K. Everett, Julie C. Mitchell, Luis C. López, Joshua J. Coon, Liang Tong, and David J. Pagliarini
Coenzyme Q (CoQ) is a requisite component of the mitochondrial oxidative phosphorylation machinery that produces more than 90% of cellular ATP. Despite the discovery of CoQ more than 50 years ago, many aspects of its biosynthesis remain obscure. These include the functions of uncharacterized CoQ-related proteins whose disruption can cause human diseases. Our work reveals that one such protein, COQ9, is a lipid-binding protein that enables CoQ biosynthesis through its physical and functional interaction with COQ7, and via its stabilization of the entire CoQ biosynthetic complex. Unexpectedly, COQ9 achieves these functions by repurposing an ancient bacterial fold typically used for transcriptional regulation. Collectively, our work (pp. E4697–E4705) adds new insight into a core component of the CoQ biosynthesis process.
VEGF-induced neoangiogenesis is mediated by NAADP and two-pore channel-2–dependent Ca2+ signaling
Annarita Favia, Marianna Desideri, Guido Gambara, Alessio D’Alessio, Margarida Ruas, Bianca Esposito, Donatella Del Bufalo, John Parrington, Elio Ziparo, Fioretta Palombi, Antony Galione, and Antonio Filippini
The formation of new blood vessels (neoangiogenesis) accompanies tissue regeneration and healing, but is also crucial for tumor growth, hence understanding how capillaries are stimulated to grow in response to local cues is essential for the much sought-after aim of controlling this process. We have elucidated a Ca2+ signaling pathway involving NAADP, TPCs, and lysosomal Ca2+ release activated in vascular endothelial cells by VEGF, the main angiogenic growth factor, and we show (pp. E4706–E4715) that the angiogenic response can be abolished, in cultured cells and in vivo, by inhibiting components of this signaling cascade. The specificity of this pathway in terms of VEGF receptor subtype, intracellular messengers, target channels and Ca2+ storage organelles, offers new targets for novel antiangiogenic therapeutic strategies.
WWOX, the common fragile site FRA16D gene product, regulates ATM activation and the DNA damage response
Mohammad Abu-Odeh, Zaidoun Salah, Christoph Herbel, Thomas G. Hofmann, and Rami I. Aqeilan
Genomic instability is a hallmark of human cancers. Common fragile sites (CFSs) pose nonrandom, preferential targets of genomic instability, such as chromosome breaks, in response to replicative stress. The tumor suppressor WW domain-containing oxidoreductase (WWOX) spans the CFS FRA16D and has been implicated in carcinogenesis by a currently unknown mechanism. In this study (pp. E4716–E4725), we identify a direct role of WWOX in DNA damage response, which is a major antagonist of genomic instability. We show that WWOX maintains genomic stability and regulates DNA repair by modulating the activity of the DNA damage checkpoint kinase ataxia telangiectasia-mutated (ATM). Our findings provide evidence that a fragile gene product is directly involved in the response to DNA damage, suggesting a rationale for its preferential loss during carcinogenesis.
Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing
Mei-Chong Wendy Lee, Fernando J. Lopez-Diaz, Shahid Yar Khan, Muhammad Akram Tariq, Yelena Dayn, Charles Joseph Vaske, Amie J. Radenbaugh, Hyunsung John Kim, Beverly M. Emerson, and Nader Pourmand
Tumor cells are heterogeneous, and much variation occurs at the single-cell level, which may contribute to therapeutic response. Here (pp. E4726–E4735), we studied drug resistance dynamics in a model of tolerance with a metastatic breast cancer cell line by leveraging the power of single-cell RNA-Seq technology. Drug-tolerant cells within a single clone rapidly express high cell-to-cell transcript variability, with a gene expression profile similar to untreated cells, and the population reacquires paclitaxel sensitivity. Our gene expression and single nucleotide variants analyses suggest that equivalent phenotypes are achieved without relying on a unique molecular event or fixed transcriptional programs. Thus, transcriptional heterogeneity might ensure survival of cancer cells with equivalent combinations of gene expression programs and/or single nucleotide variants.
Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid
M. Sabrina Pankey, Vladimir N. Minin, Greg C. Imholte, Marc A. Suchard, and Todd H. Oakley
Unless there are strong constraints, the probability of complex organs originating multiple times through similar trajectories should be vanishingly small. Here (pp. E4736–E4742), we report that similar light-producing organs (photophores) evolved separately in two squid species, yet each organ expresses similar genes at comparable levels. Gene expression is so similar that overall expression levels alone can predict organ identity, even in separately evolved traits of squid species separated by tens of millions of years. The striking similarity of expression of hundreds of genes in distinct photophores indicates complex trait evolution may sometimes be more constrained and predictable than expected, either because of internal factors, like a limited array of suitable genetic building blocks, or external factors, like natural selection favoring an optimum.
Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development
Mei-Yeh Jade Lu, Wen-Lang Fan, Woei-Fuh Wang, Tingchun Chen, Yi-Ching Tang, Fang-Hua Chu, Tun-Tschu Chang, Sheng-Yang Wang, Meng-yun Li, Yi-Hua Chen, Ze-Shiang Lin, Kai-Jung Yang, Shih-May Chen, Yu-Chuan Teng, Yan-Liang Lin, Jei-Fu Shaw, Ting-Fang Wang, and Wen-Hsiung Li
Antrodia cinnamomea, a mushroom, has long been used as a remedy for cancer, hypertension, and hangover. However, the molecular basis of its medicinal effects is unclear and its genome has not been studied. We obtained a genome draft and conducted gene annotation. Genome ontology enrichment and pathway analyses shed light on sexual development and metabolite biosynthesis. We identified genes differentially expressed between mycelium and fruiting body and also proteins in the mevalonate pathway, terpenoid pathways, cytochrome P450s, and polyketide synthases, which may contribute to production of medicinal metabolites. Genes of metabolite biosynthesis pathways showed expression enrichment for tissue-specific compounds in mycelium and in fruiting body. Our data (pp. E4743–E4752) will be useful for developing a strategy to increase the production of valuable metabolites.
Identification of 14-series sulfido-conjugated mediators that promote resolution of infection and organ protection
Jesmond Dalli, Nan Chiang, and Charles N. Serhan
Inability of the body to contain infections may lead to collateral organ damage resulting from unchecked innate immune responses. Here (pp. E4753–E4761) we investigated the chemical signals produced by immune cells to expedite clearance of bacteria and promote organ repair and tissue regeneration. We identified molecules produced during self-limited infections and in human milk that promote clearance of bacteria as well as accelerate tissue regeneration. In addition, these molecules also protected organs from exuberant inflammatory responses by limiting select white blood cell recruitment and up-regulating the expression of proteins involved in tissue repair. Therefore, these results identify new resolution moduli that regulate phagocytes to clear bacteria and activate the regeneration milieu.
Interleukin 1 receptor-associated kinase 1 (IRAK1) mutation is a common, essential driver for Kaposi sarcoma herpesvirus lymphoma
Dongmei Yang, Wuguo Chen, Jie Xiong, Carly J. Sherrod, David H. Henry, and Dirk P. Dittmer
Primary effusion lymphoma (PEL) is an AIDS-defining cancer. It is associated with Kaposi sarcoma-associated herpesvirus. To date, no sequencing studies have been conducted for this cancer. We used X chromosome-targeted next-generation sequencing to identify 33 genes with coding region mutations in 100% of cases, including in interleukin 1 receptor-associated kinase 1 (IRAK1). IRAK1 kinase modulates toll-like receptor signaling-mediated immune signaling. It binds to MyD88 adapter protein, which is mutated in a subset of diffuse large B-cell lymphomas. IRAK1, however, had not been linked to cancer. This IRAK1 mutant is constitutively active and essential for PEL survival. This highlights the importance of innate immunity signaling as drivers for cancer, particularly those caused by viruses (pp. E4762–E4768). It also suggests IRAK1 kinase may be a potential target for therapy.
Activity-dependent FUS dysregulation disrupts synaptic homeostasis
Chantelle F. Sephton, Amy A. Tang, Ashwinikumar Kulkarni, James West, Mieu Brooks, Jeremy J. Stubblefield, Yun Liu, Michael Q. Zhang, Carla B. Green, Kimberly M. Huber, Eric J. Huang, Joachim Herz, and Gang Yu
Both overexpression of wild-type fused in sarcoma (FUS) protein and missense mutations can be pathogenic in a group of related neurodegenerative disorders that includes amyotrophic lateral sclerosis and frontotemporal lobar degeneration. It is unclear how FUS overexpression and missense mutations cause disease in human patients. In this work (pp. E4769–E4778), we generated novel transgenic mouse models expressing low levels of wild-type and mutant human FUS, both of which recapitulate aspects of the human diseases. We found a profound difference in the underlying mechanisms by which missense mutation and wild-type overexpression cause disease. Overexpression of wild-type FUS protein alters its nuclear function at the level of gene expression. In contrast, missense mutation disrupts activity-dependent synaptic homeostasis to gain a toxic function at dendritic spines.
The rare DAT coding variant Val559 perturbs DA neuron function, changes behavior, and alters in vivo responses to psychostimulants
Marc A. Mergy, Raajaram Gowrishankar, Paul J. Gresch, Stephanie C. Gantz, John Williams, Gwynne L. Davis, C. Austin Wheeler, Gregg D. Stanwood, Maureen K. Hahn, and Randy D. Blakely
Dopamine (DA) signaling provides important, modulatory control of movement, at tention, and reward. Disorders linked to changes in DA signaling include Parkinson’s disease, attention-deficit hyperactivity disorder, schizophrenia, autism spectrum disorder, and addiction. We identified multiple, functional polymorphisms in the human DA transporter (DAT) gene and showed that one of these variants, which produces the amino acid substitution Val559 (wild-type DATs express Ala559), exhibits normal DA uptake accompanied by a spontaneous outward efflux of the neurotransmitter, reminiscent of the actions of the psychostimulant amphetamine. Here (pp. E4779–E4788), we identify multiple biochemical, physiological, and behavioral perturbations that arise from DAT Val559 expression in vivo, supporting spontaneous DA efflux as a heretofore-unrecognized mechanism that may underlie multiple DA-linked neurobehavioral disorders.
Chemoselective tarantula toxins report voltage activation of wild-type ion channels in live cells
Drew C. Tilley, Kenneth S. Eum, Sebastian Fletcher-Taylor, Daniel C. Austin, Christophe Dupré, Lilian A. Patrón, Rita L. Garcia, Kit Lam, Vladimir Yarov-Yarovoy, Bruce E. Cohen, and Jon T. Sack
Electrically excitable cells, such as neurons, exhibit tremendous variation in their patterns of electrical signals. These variations arise from the collection of ion channels present in any specific cell, but understanding which ion channels are at the root of particular electrical signals remains a significant challenge. Here (pp. E4789–E4796), we describe novel probes, derived from a tarantula venom peptide, that are able to report the activity of voltage-gated ion channels in living cells. This technology uses state-selective binding to optically monitor the activation of ion channels during cellular electrical signaling. Activity-reporting probes based on these prototypes could potentially identify when endogenous ion channels contribute to electrical signaling, thus facilitating the identification of ion channel targets for therapeutic drug intervention.
Time-variant clustering model for understanding cell fate decisions
Wei Huang, Xiaoyi Cao, Fernando H. Biase, Pengfei Yu, and Sheng Zhong
Clustering, in essence, was a tool for describing spatial characteristics in the objects of concern. However, from social to biological studies, researchers’ interests in temporal characteristics often rival their interests in spatial features. Previous efforts to incorporate time information into clustering primarily relied on coding the time information into similarity metrics, thus reducing the problem into the classical paradigm of spatial clustering. The limitation is that the clustering outcomes are often time invariant. Here, we initiate a class of statistical methods that simultaneously infer spatial and temporal groupings. Such methods explicitly model the time dependencies of clustering indices over time. Our method (pp. E4797–E4806) inferred three genes to be associated with the earliest cell fate decision, which was corroborated by experimental validations.